Mercurial > repos > devteam > bowtie2
changeset 27:a6d65b0c67af draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit d142d9cd5a8db8a87184c4b7622ea8de8355894f"
| author | iuc |
|---|---|
| date | Sat, 10 Jul 2021 07:45:14 +0000 |
| parents | 09b2cdb7ace5 |
| children | cd659e8cc5fa |
| files | bowtie2_macros.xml bowtie2_wrapper.xml test-data/bowtie2-test1.bam test-data/bowtie2-test2.bam test-data/bowtie2-test_fasta_in.bam test-data/bowtie2-test_fasta_in_bam_qname_input_sorted.bam test-data/bowtie2-test_il.bam |
| diffstat | 7 files changed, 4 insertions(+), 4 deletions(-) [+] |
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--- a/bowtie2_macros.xml Tue Jan 12 16:58:26 2021 +0000 +++ b/bowtie2_macros.xml Sat Jul 10 07:45:14 2021 +0000 @@ -24,7 +24,7 @@ #import itertools #set $input_name1 = $clean($identifier_or_name($input1)) #set $input_name2 = $clean($identifier_or_name($input2)) - #set $common_prefix = ''.join([c[0] for c in itertools.takewhile(lambda x: all(x[0] == y for y in x), itertools.izip(*[$input_name1, $input_name2]))]) + #set $common_prefix = ''.join([c[0] for c in itertools.takewhile(lambda x: all(x[0] == y for y in x), zip(*[$input_name1, $input_name2]))]) #if len($common_prefix) > 3 #return $common_prefix #else
--- a/bowtie2_wrapper.xml Tue Jan 12 16:58:26 2021 +0000 +++ b/bowtie2_wrapper.xml Sat Jul 10 07:45:14 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="bowtie2" name="Bowtie2" version="@TOOL_VERSION@+galaxy0" profile="18.01"> +<tool id="bowtie2" name="Bowtie2" version="@TOOL_VERSION@+galaxy0" profile="20.05"> <description>- map reads against reference genome</description> <macros> <import>bowtie2_macros.xml</import> @@ -305,9 +305,9 @@ ## output file #if str( $sam_options.sam_options_selector ) == "no" or (str( $sam_options.sam_opt ) == "false" and str($sam_options.reorder) == ''): - | samtools sort -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -O bam -o '$output' + | samtools sort --no-PG -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -O bam -o '$output' #else if $sam_options.reorder: - | samtools view -bS - -o '$output' + | samtools view --no-PG -bS - -o '$output' #else: > '$output' #end if